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AdvancedThe GCMPlugin reads some of parameters from the 'GCMPlugin.ini' textfile at startup, which should be next to the GCMPlugin dll. These parameters are 'Global' parameters, in the sense that they generally affect all computations of every map. Most the parameters finetune the computations of the Granger Causality Maps, their various compositions (e.g. dGCMs) and the bootstrapping of significance thresholds. Some parameters can be set to taste, such as: which result maps and which FDR thresholds to compute, how much feedback to give in the Logtab, and how to scale the maps for visualisation. Most computation related parameters have generally been assigned sensible or even optimal defaults, but you can change them to see what effect a different setting might have. The .ini file is anotated with commentlines (starting with '//') that explain the different parameters.If an unacceptable change is made to the .ini file, the GCMPlugin will give out a warning at startup, generally with a remark about the offending parameter. The GCMPlugin will use the default parameters, hardcoded into GCMPlugin.dll, and continue when the .ini file could not be found or was invalid. Therefore, be attentive to warnings at startup to see whether your changes did not invalidate the .ini file and were subsequently ignored. //******************************************************* // Granger causality mapping (GCM) plugin inifile // Read by the GCMPlugin to initialize global // parameters. Change only if you know what // you are doing and at your own risk! //******************************************************* // Maps that are computed for every condition, possible values (enumeration): // INST : Instanteneous GC term between reference and voxel (Geweke (1982)) // REF2VOX : Directed GC term from reference to voxel (Geweke (1982)) // VOX2REF : Directed GC term from voxel to reference (Geweke (1982)) // DGCM : The difference GCM (DGCM) = REF2VOX  VOX2REF // DGCM_IT : The dGCM, instantaneously thresholded, i.e. dGCM masked with // the thresholded instantaneous map, // i.e. DGCM_IT = DGCM, only where INST > DGCM_ITInstLowerThres (unscaled, see below) // else it is set to zero (vessels) MapTypesComputed= INST DGCM_IT DGCM_ITInstLowerThres= 0.05 // False dicovery rates (q) used to compute (multiple comparison corrected) thresholds // Listed in the map dialog QThresholdsForFDR= 0.01 0.05 0.1 // The c(V) constant (see Genovese, NI) that incorporates assumptions about the spatial // distribution of pvalues over the map. Can be 1 (c(V)=1, liberal, some assumptions), // or 2 (c(V)=sum(1:N)), conservative, but assumption free) CVConstantForFDR= 2 // Show a verbose progresslog in the Logtab while computing, when 1 // Only show limited information (e.g. written files), when 0 ShowVerboseProgressLog= 1 // All maps (except DGCM_RC that always ranges from 0 to 1) are scaled by the MapScaleFactor // This is only for convenience and visualisation purposes. The natural values of the computed // measures lie in the 0.01 range. The scalefactor may be used to put them in a more // 'intuitive' range, that works beter with display and thresholding routines in BVQX. MapScaleFactor= 100 // Order of the VAR models used to compute the Geweke (1982) measures AutoRegressionOrder= 1 // Voxels with first timepoint below FirstTimePointInclusionThres are discarded, // All GCMs are set to zero, and are not taken into account for threshold determinations FirstTimePointInclusionThres= 100 // Bootstrapping of pvalues is done by finding the fraction of more extreme values // in a surrogate NULLdistribution. The NULLdistribution is created by recomputing each // term for each voxel with a simulated NULLreference (from an AR model estimated on // the real reference). Instead of resimulating a reference for each voxel, a simulated // reference is randomly selected for each voxel from a presimulated pool of NULLrefs. // Pool has size NumSurrogateSimulations NumSurrogateSimulations= 5000 // When simulating an AR model (driven by white noise), the first part of the simulated series // has to be discarded, to get to a steady state of the model, NumDiscardedSimulatedTimePoints points // are skipped for every simulation in the presimulated pool of NULLrefs NumDiscardedSimulatedTimePoints= 100 